Cleanup datasets

Here I cleanup datasets:
-  If I don't recognize a dataset or if I know that it is incorrect, I removed it.
- I give friendly names to the remaining datasets, mostly according to what's written in their reference fasta file.
- I try to make directory structure and naming a little more consistent (it is now reflected in the dataset `path` which is used as an identifier of the dataset in many places exposed to the end user).

This is mostly a "cosmetic" change, needed for testing usability of the current Nextclade Web UI and for making it prettier.

I have little knowledge in most of these pathogens, so this PR can be rolled back and the reorganization can be done properly by a scientists later.

data/community/adenovirus/hadv-a/pathogen.json → data/community/adenovirus/hadv-a/12/pathogen.json

@@ -1,12 +1,12 @@
 {
   "attributes": {
     "name": {
-      "value": "adenovirus/hadv-a",
-      "valueFriendly": "UNKNOWN"
+      "value": "hadv-a-12",
+      "valueFriendly": "Human mastadenovirus A (serotype 12)"
     },
     "reference": {
-      "value": "UNKNOWN",
-      "valueFriendly": "UNKNOWN"
+      "value": "NC_001460.1",
+      "valueFriendly": "HAdV-A serotype 12"
     }
   },
   "compatibility": {

data/community/collection.json

@@ -15,6 +15,6 @@
     ]
   },
   "dataset_order": [
-    "community/adenovirus/hadv-a"
+    "community/adenovirus/hadv-a/12"
   ]
 }

data/nextstrain/collection.json

@@ -22,63 +22,24 @@
   },
   "dataset_order": [
     "nextstrain/sars-cov-2/MN908947",
-    "nextstrain/sars-cov-2-21L/BA.2",
-    "nextstrain/MPXV/ancestral",
-    "nextstrain/hMPXV/NC_063383.1",
-    "nextstrain/hMPXV_B1/pseudo_ON563414",
-    "nextstrain/rsv_a/EPI_ISL_412866",
-    "nextstrain/rsv_b/EPI_ISL_1653999",
-    "nextstrain/flu_h1n1pdm_ha/CY121680",
-    "nextstrain/flu_h1n1pdm_ha/MW626062",
-    "nextstrain/flu_h1n1pdm_na/MW626056",
-    "nextstrain/flu_h3n2_ha/CY163680",
-    "nextstrain/flu_h3n2_ha/EPI1857216",
-    "nextstrain/flu_h3n2_na/EPI1857215",
-    "nextstrain/flu_vic_ha/KX058884",
-    "nextstrain/flu_vic_na/CY073894",
-    "nextstrain/flu_yam_ha/JN993010",
-    "nextstrain/sars-cov-2-no-recomb/MN908947",
-    "nextstrain/dummy1",
-    "nextstrain/h1_na",
-    "nextstrain/hbv",
-    "nextstrain/hiv",
-    "nextstrain/hiv_mat",
-    "nextstrain/rsv-a",
-    "nextstrain/sc2",
-    "nextstrain/sc2-big",
-    "nextstrain/sc2_mat",
-    "nextstrain/vic_na",
-    "nextstrain/ebola",
-    "nextstrain/enterovirus/d68",
-    "nextstrain/flu/h1n1pdm/ha",
-    "nextstrain/flu/h1n1pdm/na",
-    "nextstrain/flu/h1n1pdm/np",
-    "nextstrain/flu/h1n1pdm/ns",
-    "nextstrain/flu/h1n1pdm/pa",
-    "nextstrain/flu/h1n1pdm/pb1",
-    "nextstrain/flu/h1n1pdm/pb2",
-    "nextstrain/flu/h3n2/ha",
-    "nextstrain/flu/h3n2/ma",
-    "nextstrain/flu/h3n2/na",
-    "nextstrain/flu/h3n2/np",
-    "nextstrain/flu/h3n2/ns",
-    "nextstrain/flu/h3n2/pa",
-    "nextstrain/flu/h3n2/pb1",
-    "nextstrain/flu/h3n2/pb2",
-    "nextstrain/flu/vic/ha",
-    "nextstrain/flu/vic/na",
-    "nextstrain/flu/vic/np",
-    "nextstrain/flu/vic/ns",
-    "nextstrain/flu/vic/pa",
-    "nextstrain/flu/vic/pb1",
-    "nextstrain/flu/vic/pb2",
-    "nextstrain/flu/yam/ha",
-    "nextstrain/flu/yam/na",
-    "nextstrain/flu/yam/np",
-    "nextstrain/flu/yam/ns",
-    "nextstrain/flu/yam/pa",
-    "nextstrain/flu/yam/pb1",
-    "nextstrain/flu/yam/pb2",
-    "nextstrain/zika"
+    "nextstrain/sars-cov-2/BA.2",
+    "nextstrain/flu/h1n1pdm/ha/CY121680",
+    "nextstrain/flu/h1n1pdm/ha/MW626062",
+    "nextstrain/flu/h1n1pdm/na/MW626056",
+    "nextstrain/flu/h3n2/ha/CY163680",
+    "nextstrain/flu/h3n2/ha/EPI1857216",
+    "nextstrain/flu/h3n2/na/EPI1857215",
+    "nextstrain/flu/vic/ha/KX058884",
+    "nextstrain/flu/vic/na/CY073894",
+    "nextstrain/flu/yam/ha/JN993010",
+    "nextstrain/rsv/a/EPI_ISL_412866",
+    "nextstrain/rsv/b/EPI_ISL_1653999",
+    "nextstrain/mpx/hmpxv-b1/pseudo_ON563414",
+    "nextstrain/mpx/hmpxv/NC_063383.1",
+    "nextstrain/mpx/mpxv/ancestral",
+    "nextstrain/ebola/zaire",
+    "nextstrain/enterovirus/d68/fermon",
+    "nextstrain/hiv/1",
+    "nextstrain/zika/KX369547.1"
   ]
 }

data/nextstrain/ebola/pathogen.json → data/nextstrain/ebola/zaire/pathogen.json

@@ -2,11 +2,11 @@
   "attributes": {
     "name": {
       "value": "ebola",
-      "valueFriendly": "UNKNOWN"
+      "valueFriendly": "Zaire ebolavirus"
     },
     "reference": {
-      "value": "UNKNOWN",
-      "valueFriendly": "UNKNOWN"
+      "value": "KR075003.1",
+      "valueFriendly": "LBR/2014/Makona-Liberia-DQE14"
     }
   },
   "compatibility": {

data/nextstrain/flu/h1n1pdm/na/pathogen.json → data/nextstrain/enterovirus/d68/fermon/pathogen.json

@@ -1,12 +1,12 @@
 {
   "attributes": {
     "name": {
-      "value": "flu/h1n1pdm/na",
-      "valueFriendly": "UNKNOWN"
+      "value": "ev-d68-fermon",
+      "valueFriendly": "Human enterovirus D68"
     },
     "reference": {
-      "value": "UNKNOWN",
-      "valueFriendly": "UNKNOWN"
+      "value": "AY426531.1",
+      "valueFriendly": "EV-D68 strain Fermon"
     }
   },
   "compatibility": {